Buggy code:
public class AtomCache { public static final String BIOL_ASSEMBLY_IDENTIFIER = "BIO:" ; public static final String CHAIN_NR_SYMBOL = ":" ; public static final String CHAIN_SPLIT_SYMBOL = "." ; public static final String PDP_DOMAIN_IDENTIFIER = "PDP:" ; public static final Pattern scopIDregex = Pattern . compile ( "d(....)(.)(.)" ) ; public static final String UNDERSCORE = "_" ; private static final String FILE_SEPARATOR = System . getProperty ( "file.separator" ) ; private boolean fetchCurrent ; private boolean fetchFileEvenIfObsolete ; protected FileParsingParameters params ; protected PDPProvider pdpprovider ; boolean autoFetch ; String cachePath ; Collection < String > currentlyLoading = Collections . synchronizedCollection ( new TreeSet < String > ( ) ) ; boolean isSplit ; String path ; boolean strictSCOP ; boolean useMmCif ; public AtomCache ( ) { } public AtomCache ( String pdbFilePath , boolean isSplit ) { } public AtomCache ( UserConfiguration config ) { } public Atom [ ] getAtoms ( String name ) throws IOException , StructureException { } @ Deprecated public Atom [ ] getAtoms ( String name , boolean clone ) throws IOException , StructureException { } public Structure getBiologicalAssembly ( String pdbId , int bioAssemblyId , boolean bioAssemblyFallback ) throws IOException , StructureException { } public Structure getBiologicalUnit ( String pdbId ) throws IOException , StructureException { } public String getCachePath ( ) { } public FileParsingParameters getFileParsingParams ( ) { } public String getPath ( ) { } public PDPProvider getPdpprovider ( ) { } public Structure getStructure ( String name ) throws IOException , StructureException { if ( ( name . length ( ) ) < 4 ) { <START_BUG> throw new IllegalArgumentException ( "Can't<seq2seq4repair_space>interpret<seq2seq4repair_space>IDs<seq2seq4repair_space>that<seq2seq4repair_space>are<seq2seq4repair_space>shorter<seq2seq4repair_space>than<seq2seq4repair_space>4<seq2seq4repair_space>residues!" ) ; <END_BUG> } Structure n = null ; boolean useChainNr = false ; boolean useDomainInfo = false ; String range = null ; int chainNr = - 1 ; try { StructureName structureName = new StructureName ( name ) ; String pdbId = null ; String chainId = null ; if ( ( name . length ( ) ) == 4 ) { pdbId = name ; Structure s ; if ( useMmCif ) { s = loadStructureFromCifByPdbId ( pdbId ) ; } else { s = loadStructureFromPdbByPdbId ( pdbId ) ; } return s ; } else if ( structureName . isScopName ( ) ) { return getStructureFromSCOPDomain ( name ) ; } else if ( structureName . isCathID ( ) ) { return getStructureForCathDomain ( structureName , CathFactory . getCathDatabase ( ) ) ; } else if ( ( name . length ( ) ) == 6 ) { pdbId = name . substring ( 0 , 4 ) ; if ( name . substring ( 4 , 5 ) . equals ( AtomCache . CHAIN_SPLIT_SYMBOL ) ) { chainId = name . substring ( 5 , 6 ) ; } else if ( name . substring ( 4 , 5 ) . equals ( AtomCache . CHAIN_NR_SYMBOL ) ) { useChainNr = true ; chainNr = Integer . parseInt ( name . substring ( 5 , 6 ) ) ; } } else if ( ( name . startsWith ( "file://" ) ) || ( name . startsWith ( "http://" ) ) ) { try { URL url = new URL ( name ) ; return getStructureFromURL ( url ) ; } catch ( Exception e ) { e . printStackTrace ( ) ; return null ; } } else if ( structureName . isPDPDomain ( ) ) { try { return getPDPStructure ( name ) ; } catch ( Exception e ) { e . printStackTrace ( ) ; return null ; } } else if ( name . startsWith ( AtomCache . BIOL_ASSEMBLY_IDENTIFIER ) ) { try { return getBioAssembly ( name ) ; } catch ( Exception e ) { e . printStackTrace ( ) ; return null ; } } else if ( ( ( ( ( name . length ( ) ) > 6 ) && ( ! ( name . startsWith ( AtomCache . PDP_DOMAIN_IDENTIFIER ) ) ) ) && ( ( name . contains ( AtomCache . CHAIN_NR_SYMBOL ) ) || ( name . contains ( AtomCache . UNDERSCORE ) ) ) ) && ( ! ( ( name . startsWith ( "file://" ) ) || ( name . startsWith ( "http://" ) ) ) ) ) { pdbId = name . substring ( 0 , 4 ) ; useDomainInfo = true ; range = name . substring ( 5 ) ; } if ( pdbId == null ) { return null ; } while ( checkLoading ( pdbId ) ) { try { Thread . sleep ( 100 ) ; } catch ( InterruptedException e ) { System . err . println ( e . getMessage ( ) ) ; } } Structure s ; if ( useMmCif ) { s = loadStructureFromCifByPdbId ( pdbId ) ; } else { s = loadStructureFromPdbByPdbId ( pdbId ) ; } if ( ( ( chainId == null ) && ( chainNr < 0 ) ) && ( range == null ) ) { n = StructureTools . getReducedStructure ( s , ( - 1 ) ) ; } else { if ( useChainNr ) { n = StructureTools . getReducedStructure ( s , chainNr ) ; } else if ( useDomainInfo ) { n = StructureTools . getSubRanges ( s , range ) ; } else { n = StructureTools . getReducedStructure ( s , chainId ) ; } } } catch ( Exception e ) { System . err . println ( ( "problem<seq2seq4repair_space>loading:" + name ) ) ; e . printStackTrace ( ) ; throw new StructureException ( ( ( ( e . getMessage ( ) ) + "<seq2seq4repair_space>while<seq2seq4repair_space>parsing<seq2seq4repair_space>" ) + name ) , e ) ; } n . setName ( name ) ; return n ; } public Structure getStructureForDomain ( ScopDomain domain ) throws IOException , StructureException { }

Fix:
throw new IllegalArgumentException ( "Can't<seq2seq4repair_space>interpret<seq2seq4repair_space>IDs<seq2seq4repair_space>that<seq2seq4repair_space>are<seq2seq4repair_space>shorter<seq2seq4repair_space>than<seq2seq4repair_space>4<seq2seq4repair_space>characters!" ) ;